Public-health experts traditionally track the spread of an infectious disease through clinical data such as test results, hospitalizations and deaths. As Covid-19 continues to spread, scientists are turning to an alternative measure: wastewater analysis. SARS-CoV-2, the virus that causes Covid-19, can be shed in an infected person’s feces. By sampling sewage at waste-treatment plants, scientists can get a picture of how widespread Covid-19 has become in a community, and how its prevalence changes over time.
The extent of Covid-19 testing has varied throughout the pandemic. Because wastewater can be sampled at regular intervals, it may provide a reliable adjunct to data from clinical tests.
How Researchers Collect Virus Samples from Wastewater
Samples can be collected at several points along the sewage network.
People infected with the SARS-CoV-2 can shed the virus through their feces.
‘Targeted surveillance’ focuses on smaller populations and happens closer to the source, such as a university or prison. Samples can be collected from nearby manholes.
Samples can be collected in two forms at facilities.
‘Community surveillance’ is used to evaluate infection trends within the larger community. Samples are collected at the wastewater treatment facility.
‘Untreated wastewater’ contains feces and waste from other sources such as rainwater.
‘Primary sludge’ comprises solids that settle out of wastewater during the ‘sedimentation’ process. Viral particles are more concentrated in sludge, meaning less volume is
needed for analysis.
Samples can be collected at several points along the sewage network.
People infected with the SARS-CoV-2 can shed the virus through their feces.
‘Targeted surveillance’ focuses on smaller populations and happens closer to the source, such as a university or prison. Samples can be collected from nearby manholes.
‘Community surveillance’ is used to evaluate infection trends within the larger community. Samples are collected at the wastewater treatment facility.
Samples can be collected in two forms at facilities.
‘Untreated wastewater’ contains
feces and waste from other sources such as rainwater.
‘Primary sludge’ comprises solids that settle out of wastewater during the ‘sedimentation’ process. Viral particles are more concentrated in sludge, meaning less volume is needed for analysis.
People infected with the SARS-CoV-2 can shed the virus through their feces.
Samples can be collected at several points along the sewage network.
‘Targeted surveillance’ focuses on smaller populations and happens closer to the source, such as a university or prison. Wastewater can be collected from nearby manholes.
‘Community surveillance’ is used to evaluate infection trends within the larger community. Samples are collected at the wastewater treatment facility.
Samples can be collected in two forms at facilities.
‘Untreated wastewater’ contains
feces and waste from other sources such as rainwater.
‘Primary sludge’ comprises solids that settle out of wastewater during the ‘sedimentation’ process. Viral particles are more concentrated in sludge, meaning less volume is needed for analysis.
The method has previously been used to track other pathogens, such as the virus that causes polio, as well as use of illegal drugs. Data from wastewater analysis often tracks closely with data compiled from lab results.
How Sars-Cov-2 concentrations in U.S. wastewater compare with data from clinical tests
Wastewater
SARS-CoV-2 concentration
(virus copies/ml of sewage)
Clinical
New daily cases per
100,000 people
How Sars-Cov-2 concentrations in U.S.
wastewater compare with data from clinical tests
Wastewater
SARS-CoV-2 concentration
(virus copies/ml of sewage)
Clinical
New daily cases per
100,000 people
How Sars-Cov-2 concentrations in U.S.
wastewater compare with data from
clinical tests
Wastewater
SARS-CoV-2
concentration
(virus copies/ml of sewage)
Clinical
New daily
cases per
100,000 people
Wastewater testing can also offer early signs of a Covid-19 uptick. Patients can shed the virus in their feces before they develop symptoms and think to get tested, so evidence of an outbreak may first show up in the sewers.
Mariana Matus, chief executive and co-founder of Biobot Analytics, says wastewater analysis is most effective at early detection within smaller populations before disease is widespread. “Its most important application as a leading indicator is in small communities,” she said, such as dormitories, nursing homes and prisons.
By genetically analyzing sewage samples, scientists are also able to track the rise and fall of individual Covid-19 variants.
Genomic sequencing of wastewater showed the Delta variant rapidly gaining ground in the U.S. during the summer. This rise preceded an increase in the actual concentration of SARS-CoV-2 in wastewater. Dr. Matus said that suggests there is an offset of a few weeks between the rise of Delta and the rise in disease transmission.
Presence of the SARS-CoV-2 virus in wastewater samples
Delta variant prevalence
In wastewater samples
Total SARS-CoV-2 concentration
virus copies per ml in wastewater*
Presence of the SARS-CoV-2 virus in
wastewater samples
Delta variant
prevalence
In wastewater
samples
Total SARS-CoV-2
concentration
virus copies per
ml in wastewater*
Presence of the SARS-CoV-2 virus in
wastewater samples
Delta variant
prevalence
In wastewater
samples
Total SARS-CoV-2
concentration
virus copies per
ml in wastewater*
The Centers for Disease Control and Prevention said Monday that Omicron is now the dominant variant in the U.S., surpassing Delta. In the week ended Dec. 18, Omicron’s prevalence reached 73% in the U.S., up from a revised figure of 13% a week earlier. In the New York/New Jersey region, the figure topped 90%.
Prevalence of SARS-CoV-2 variants for weeks ending in the date shown
Prevalence of SARS-CoV-2 variants for weeks ending
in the date shown
Sewage testing is often effective in the early stages of an outbreak. “Generally, wastewater is a leading indicator when the disease prevalence is very low,” said Dr. Matus.
Last spring, the Delta variant was detected at Houston’s wastewater treatment plants weeks before the first clinical cases were confirmed in the city.
Detection of the Delta variant in Houston wastewater plants, weekly data
WASTEwater PLANTS (Ordered by size of population served, from top to bottom) ▶
May 24
Health dept. receives first
report of Delta variant case
Detection of the Delta variant in Houston
wastewater plants, weekly data
WASTEwater PLANTS (Ordered by size of population served, from top to bottom) ▶
May 24
Health dept. receives first
report of Delta variant case
Detection of the Delta variant in
Houston wastewater plants,
weekly data
WASTEwater PLANTS (Ordered by size of population served, from top to bottom) ▶
May 24
Health dept. receives first
report of Delta variant case
More recently, the city had its first lab-confirmed case of the Omicron variant Dec. 9. But the variant was detected in Houston wastewater collected about 10 days earlier.
Similarly, scientists from the Sewer Coronavirus Alert Network (SCAN) detected Omicron in Merced, Calif., wastewater collected Nov. 25, before the state’s first positive clinical case was identified Dec. 1. SCAN processes samples daily from 12 wastewater treatment plants in Northern California.
—Alberto Cervantes contributed to this article.
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